reactivate sh; polish subtraction

newest/mk150.sh

@@ -27,7 +27,7 @@ OUTFOLDER=150
 OUTBASENAME=snpEff_${OUTFOLDER}_summary
 
 DOFIX=0
-DOSNPEFF=0
+DOSNPEFF=1
 DOMERGE=1
 
 
@@ -198,12 +198,12 @@ if [[ "$DOSNPEFF" ]]; then
 
     if [[ ! -d "150/$bn" ]]; then
         echo "RUNNING SNPEFF FOR $bn"
-        #mkdir 150/$bn
+        mkdir 150/$bn
         cd 150/$bn
         echo $PWD
 
         #java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -c $P/snpEff.config ${REFNAME} -v <(gunzip -c $vcf) > $bn.snpeff.vcf 2>log.log
-        #gunzip -c $vcf | java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -csvStats -c $P/snpEff.config ${REFNAME} -v > $bn.snpeff.vcf 2>log.log
+        gunzip -c $vcf | java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -csvStats -c $P/snpEff.config ${REFNAME} -v > $bn.snpeff.vcf 2>log.log
 
 
 

newest/renamer.lst

 s/snpeff_dev\/snpEff3\///g
 
+s/150\/RF_000_Heinz.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Heinz 1706 LA 4345 (000)/g
 s/150\/RF_001_SZAXPI008746-45.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Moneymaker LYC 2524 (001)/g
 s/150\/RF_002_SZAXPI009284-57.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Alisa Craig (002)/g
 s/150\/RF_003_SZAXPI009285-62.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Garderners Delight PI 406760 (003)/g

newest/run.sh

@@ -11,12 +11,12 @@ REFNAME=$1
 
     if [[ ! -d "150/$bn" ]]; then
         echo "RUNNING SNPEFF FOR $bn"
-        #mkdir 150/$bn
+        mkdir 150/$bn
         cd 150/$bn
         echo $PWD
 
         #java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -c $P/snpEff.config ${REFNAME} -v <(gunzip -c $vcf) > $bn.snpeff.vcf 2>log.log
-        #gunzip -c $vcf | java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -csvStats -c $P/snpEff.config ${REFNAME} -v > $bn.snpeff.vcf 2>log.log
+        gunzip -c $vcf | java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -csvStats -c $P/snpEff.config ${REFNAME} -v > $bn.snpeff.vcf 2>log.log
 
 
 

renamer.lst

 s/snpeff_dev\/snpEff3\///g
 
+s/150\/RF_000_Heinz.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Heinz 1706 LA 4345 (000)/g
 s/150\/RF_001_SZAXPI008746-45.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Moneymaker LYC 2524 (001)/g
 s/150\/RF_002_SZAXPI009284-57.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Alisa Craig (002)/g
 s/150\/RF_003_SZAXPI009285-62.vcf.gz\/snpEff_summary.csv/S lycopersicum cv Garderners Delight PI 406760 (003)/g

scripts/median_polish/median_polish.py

@@ -143,7 +143,12 @@ if __name__ == "__main__":
 			"lycopersicum.01.tsv", "lycopersicum.02.tsv", "lycopersicum.03.tsv", "lycopersicum.04.tsv", 
 			"lycopersicum.05.tsv", "lycopersicum.06.tsv", "lycopersicum.07.tsv", "lycopersicum.08.tsv",
 			"lycopersicum.09.tsv", "lycopersicum.10.tsv", "lycopersicum.11.tsv", "lycopersicum.12.tsv",
-			"lycopersicum.tsv"]
+			"lycopersicum.tsv",
+			"lycopersicum_subtract.01.tsv", "lycopersicum_subtract.02.tsv", "lycopersicum_subtract.03.tsv", "lycopersicum_subtract.04.tsv", 
+			"lycopersicum_subtract.05.tsv", "lycopersicum_subtract.06.tsv", "lycopersicum_subtract.07.tsv", "lycopersicum_subtract.08.tsv",
+			"lycopersicum_subtract.09.tsv", "lycopersicum_subtract.10.tsv", "lycopersicum_subtract.11.tsv", "lycopersicum_subtract.12.tsv",
+			"lycopersicum_subtract.tsv"
+			]
 
 	#data_files = [	"youtube.csv"]